Anonymous Monk,
Unfortunately, the input record seperator $/ can not be a regex (at least not in Perl5). It appears that your records are two lines where the second line is what you actually care about. Try something like this:

while ( <INFILE> ) {
    my $record = <INFILE>;
    # stuff goes here
}
[download]

This way, each time through the loop $_ contains your information line of the record and $record contains the DNA sequence.

Cheers - L~R